Inactive Mu-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound#020_E1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9mqi
Q-score: 0.352
Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbolle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK
bioRxiv (2025) [ Pubmed: 39868130 DOI: doi:10.1101/2025.01.09.632033 ]
- Mu-type opioid receptor (46 kDa, Protein from Homo sapiens)
- Human mu-opioid receptor (46 MDa, Complex from Homo sapiens)
- Nabfab light chain (23 kDa, Protein from synthetic construct)
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Nabfab heavy chain (25 kDa, Protein from synthetic construct)
- Methyl (1s,3r,4s,6s,8m)-2-[(1-ethyl-1h-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)-3,4-dimethyl-2-azabicyclo[2.2.2]oct-7-ene-6-carboxylate (395 Da, Ligand)
Inactive Kappa-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound #020_E1
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 9mqk
Q-score: 0.466
Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbolle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK
bioRxiv (2025) [ Pubmed: 39868130 DOI: doi:10.1101/2025.01.09.632033 ]
- Kappa-opioid receptor (43 kDa, Protein from Homo sapiens)
- Nabfab light chain (23 kDa, Protein from synthetic construct)
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Nabfab heavy chain (25 kDa, Protein from synthetic construct)
- Methyl (1s,3r,4s,6s,8m)-2-[(1-ethyl-1h-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)-3,4-dimethyl-2-azabicyclo[2.2.2]oct-7-ene-6-carboxylate (395 Da, Ligand)
- Human kappa-opioid receptor (46 MDa, Complex from Homo sapiens)
Integrin alpha-5 beta-1 in complex with BIIG2 Fab
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9b9j
Q-score: 0.589
Nguyen A, Heim JB, Cordara G, Chan MC, Johannesen H, Charlesworth C, Li M, Azumaya CM, Madden B, Krengel U, Meves A, Campbell MG
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.08.631572 Pubmed: 39829743 ]
- Integrin alpha-5 light chain (108 kDa, Protein from Homo sapiens)
- Biig2 fab light chain (23 kDa, Protein from Rattus norvegicus)
- Biig2 fab heavy chain (23 kDa, Protein from Rattus norvegicus)
- Integrin beta-1 (80 kDa, Protein from Homo sapiens)
- Protein complex of integrin alpha-5 beta-1 with biig2 fab (Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Integrin alpha-5 beta-1 in complex with MINT1526A Fab
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b9k
Q-score: 0.547
Nguyen A, Heim JB, Cordara G, Chan MC, Johannesen H, Charlesworth C, Li M, Azumaya CM, Madden B, Krengel U, Meves A, Campbell MG
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.08.631572 Pubmed: 39829743 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Integrin alpha-5 light chain (108 kDa, Protein from Homo sapiens)
- Mint1526a fab heavy chain (13 kDa, Protein from unidentified)
- Protein complex of integrin alpha-5 beta-1 with mint1526a fab (Complex from Homo sapiens)
- Integrin beta-1 (80 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Mint1526a fab light chain (11 kDa, Protein from unidentified)
G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 9cq4
Q-score: 0.464
Hoque M, Grigg JB, Ramlall T, Jones J, McGoldrick LL, Lin JC, Olson WC, Smith E, Franklin MC, Zhang T, Saotome K
Nat Commun (2025) 16 pp. 318-318 [ Pubmed: 39747888 DOI: doi:10.1038/s41467-024-55467-5 ]
- Okt3 fab light chain (23 kDa, Protein from Mus musculus)
- T-cell surface glycoprotein cd3 zeta chain (19 kDa, Protein from Homo sapiens)
- G115 tcr gamma chain (33 kDa, Protein from Homo sapiens)
- G115 gamma delta tcr/cd3 complex bound by okt3 fab (Complex from Homo sapiens)
- Okt3 fab heavy chain (25 kDa, Protein from Mus musculus)
- G115 tcr delta chain (31 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 epsilon chain (23 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 gamma chain (20 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- T-cell surface glycoprotein cd3 delta chain (19 kDa, Protein from Homo sapiens)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9c44
Q-score: 0.535
Liu P, Huang ML, Guo H, McCallum M, Si JY, Chen YM, Wang CL, Yu X, Shi LL, Xiong Q, Ma CB, Bowen JE, Tong F, Liu C, Sun YH, Yang X, Chen J, Guo M, Li J, Corti D, Veesler D, Shi ZL, Yan H
Nature (2024) 635 pp. 978-986 [ DOI: doi:10.1038/s41586-024-08121-5 Pubmed: 39478224 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S2l20 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 s bound by s2l20 fab (Complex from Homo sapiens)
- S2l20 fab heavy chain variable (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9c45
Q-score: 0.552
Liu P, Huang ML, Guo H, McCallum M, Si JY, Chen YM, Wang CL, Yu X, Shi LL, Xiong Q, Ma CB, Bowen JE, Tong F, Liu C, Sun YH, Yang X, Chen J, Guo M, Li J, Corti D, Veesler D, Shi ZL, Yan H
Nature (2024) 635 pp. 978-986 [ DOI: doi:10.1038/s41586-024-08121-5 Pubmed: 39478224 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S2l20 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 s bound by s2l20 fab (Complex from Homo sapiens)
- S2l20 fab heavy chain variable (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of the semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9axl
Q-score: 0.473
Wang L, Wang J, Li J, Walz T, Coller BS
Blood Adv (2024) 8 pp. 4398-4409 [ DOI: doi:10.1182/bloodadvances.2024013177 Pubmed: 38968144 ]
- Magnesium ion (24 Da, Ligand)
- Integrin beta-3 (87 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- The semi-extended alphaiibbeta3 in complex with r21d10 fab (250 kDa, Complex)
- Integrin alpha-iib (113 kDa, Protein from Homo sapiens)
- R21d10 fab heavy chain (24 kDa, Protein from Mus musculus)
- Calcium ion (40 Da, Ligand)
- R21d10 fab light chain (23 kDa, Protein from Mus musculus)
The map of the bent AlphaIIbBeta3 in complex with R21D10 Fab
Wang L, Wang J, Li J, Walz T, Coller BS
Blood Adv (2024) 8 pp. 4398-4409 [ DOI: doi:10.1182/bloodadvances.2024013177 Pubmed: 38968144 ]
- R21d10 fab heavy chain (Protein from Mus musculus)
- Alphaiibbeta3 integrin (Complex from Homo sapiens)
- R21d10 fab (Complex from Mus musculus)
- The semi-extended alphaiibbeta3 in complex with r21d10 fab (250 kDa, Complex)
- Integrin beta3 (Protein from Homo sapiens)
- R211010 fab light chain (Protein from Mus musculus)
- Integrin alphaiib (Protein from Homo sapiens)
Composite cryoEM map of CD20 in complex with wild type Rituximab Fab
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8vgn
Q-score: 0.549
Kung JE, Johnson MC, Jao CC, Arthur CP, Tegunov D, Rohou A, Sudhamsu J
bioRxiv (2024) [ Pubmed: 38798381 DOI: doi:10.1101/2024.05.10.593593 ]
- Rituximab fab light chain (23 kDa, Protein from Homo sapiens)
- Rituximab fab heavy chain (24 kDa, Protein from Homo sapiens)
- Cd20 in complex with rituximab fab (Complex)
- Rituximab fab (Complex from Homo sapiens)
- B-lymphocyte antigen cd20 (31 kDa, Protein from Homo sapiens)
- Cd20 (Complex from Homo sapiens)